Explore AI Agent Skills & Claude Prompts

Use when Stereo-seq or STOmics data needs cell-cell interaction, CCI, ligand-receptor, sender-receiver, niche interaction, CellChat, CellPhoneDB, NicheNet, STcomm, SPIDER, COMMOT, stMLnet, or spatially variable ligand-receptor analysis.

stereo-seq-cell-type-mapping

Use when analyzing Stereo-seq or STOmics spatial transcriptomics data to annotate or map bin, spot, or cellbin units to cell types or cell states using marker genes, sc/snRNA references, RCTD, SPOTlight, cell2location, Tangram, SingleR, or related label-transfer and deconvolution workflows.

stereo-seq-cellbin-segmentation

Use when Stereo-seq/STOmics or subcellular spatial transcriptomics data needs cellbin generation, cell segmentation, nuclei/cell masks, ssDNA/DAPI/histology-image alignment, boundary-based expression aggregation, bin-to-cell conversion, segmentation QC, STCellbin, BIDCell, CellSPA, UCS, bin2cell, Thor, or cell-level histology integration.

stereo-seq-developmental-trajectory

Use when Stereo-seq or STOmics data needs developmental, regeneration, temporal, pseudotime, RNA velocity, lineage-flow, cell-state transition, or stage-to-stage trajectory analysis and paper-quality trajectory plots.

stereo-seq-image-registration

Use when Stereo-seq or STOmics expression coordinates, heatmaps, GEM/GEF-derived spatial maps, ssDNA, DAPI, nuclei, histology, HE, IF, tissue masks, cell masks, or image tiles need image-to-expression registration, transform application, landmark/template matching QC, affine/TPS coordinate warping, registered overlay checks, or handoff to STCellbin/GEM3D/Thor-style image-expression integration.

stereo-seq-project-orchestration

Use when a Stereo-seq or STOmics project has multiple samples, serial sections, batches, time points, conditions, donors, replicates, or mixed h5ad/RDS/GEM outputs and needs sample-sheet validation, project metadata design, multi-sample QC summaries, batch/integration handoff, or cross-sample workflow orchestration before downstream Stereo-seq skills.

stereo-seq-publication-plotting

Use when Stereo-seq or STOmics analysis needs paper-quality figures, spatial maps, dot plots, heatmaps, marker panels, module-score maps, legends, palettes, Arial typography, non-overlapping labels, or reuse of plotting code from public Stereo-seq article repositories.

stereo-seq-publication-story

Use whenever a Stereo-seq/STOmics/spatial transcriptomics request asks to reuse, cite, report, compare, or learn from real published Stereo-seq papers, paper templates, article-derived workflows, manuscript figure logic, publication story, scientific story, paper experience, provenance, DOI, code/data source, or "which paper/template was reused". Also use for Chinese requests mentioning 真实论文, 文章模板, 论文模板, story templates, 论文故事线, 复用论文经验, 复用了哪些论文, 原始论文 DOI, 代码/数据来源, 发育图谱, 器官发生, mouse embryo, organogenesis, developmental atlas, or when designing a paper-style analysis plan from a new Stereo-seq dataset. This skill searches bundled unified paper profiles before mapping to local Stereo-seq analysis/plotting skills.

stereo-seq-quality-control-preprocessing

Use when Stereo-seq or STOmics data needs QC, preprocessing, raw GEM/GEF/SAW loading, raw-to-count-matrix export, binning, bin/cell filtering, mitochondrial/count/gene QC maps, StereoPy output handling, GEM-to-Seurat conversion, or export of cleaned h5ad/RDS objects before downstream analysis.

stereo-seq-spatial-grn-regulon

Use when Stereo-seq or STOmics spatial transcriptomics data needs gene regulatory network, transcription-factor, regulon, pySCENIC/SCENIC, SpaGRN, AUCell, regulon specificity score, or spatial TF activity analysis and paper-quality regulon plots.

stereo-seq-statistical-design

Use when Stereo-seq/STOmics analysis needs replicate-aware statistical design, condition comparisons, treatment/disease/control inference, pseudobulk DEG, donor/sample/batch-aware models, spatial-domain or cell-type proportion comparisons, mixed-model design checks, graph/spatial organization metrics across conditions, or warnings about pseudo-replication before claiming differential biology.

stereo-seq-3d-reconstruction

Use when Stereo-seq or STOmics serial sections need multi-slice registration, 3D coordinate reconstruction, slice-to-atlas alignment, shape/contour matching, SABench-informed alignment method choice, or 3D-ready visualization and mapping.